U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 8003.1 

___________________________________________________________________ 

1

Sampling Options for CWD Herd Certification Plan Compliant Herd Owners to Replace a Missed 

Mortality or Poor-Quality Sample Submission 

1. Purpose and Background 

This document provides a live animal chronic wasting disease (CWD) testing option for 

farmed white-tailed deer herd owners (referred to as owners hereafter) enrolled in the 

Chronic Wasting Disease Herd Certification Program (CWD HCP)1. State animal health 

officials (SAHOs) can provide this guidance to owners who otherwise comply with the CWD 

HCP requirements but have infrequent missed mortalities or poor-quality samples. 

Animal and Plant Health Inspection Service (APHIS) regulations require certain cervid species 

moving interstate, other than for slaughter or research, be enrolled in the CWD HCP. The 

HCP provides a consistent national approach to controlling CWD in farmed cervids and 

prevents the interstate spread of the disease. To be enrolled in the CWD HCP, owners must 

conduct CWD sampling on all deaths of all cervids aged 12 months or older that occur onfarm, at slaughter, or at a hunt facility under the same ownership. Occasionally owners with 

herds in the CWD HCP have missed mortalities or submitted poor-quality samples. In 

response to this issue, APHIS developed a live animal testing option SAHOs can use in whitetailed deer herds when CWD samples are missed or of poor quality. 

APHIS statisticians calculated the number of live white-tailed deer to biopsy to equal the 

diagnostic value of an on-farm mortality. To derive this number, they calculated the 

probability of detecting CWD in an on-farm mortality using immunohistochemistry (IHC) 

testing of the medial retropharyngeal lymph nodes and obex and compared it to the 

probability of detecting CWD in a live animal by rectal anal mucosal associated lymphoid 

tissue (RAMALT) biopsy using IHC. They also examined factors such as the proportion of

positive mortalities in CWD-positive herds before depopulation2, within-herd CWD 

prevalence at depopulation3, sensitivity of on-farm mortality IHC testing4, sensitivity of live 

animal IHC testing by genotype at codon 965, and size of the herd to be sampled. The 

proportion of white-tailed deer CWD-positive exclusively in the medial retropharyngeal 

lymph node, indicating the animal was in an early stage of infection, was incorporated into 

1 This program includes both herds directly enrolled in the CWD Herd Certification Program and herds included based on their 

participation in Approved State CWD Herd Certification Programs. These are programs operated by State governments for CWD 

certification of cervid herds the Administrator has determined to meet the requirements of title 9, Code of Federal Regulations 

(9 CFR) 55.23(a). 2 For herds APHIS depopulated due to CWD, APHIS calculated the number of mortalities occurring from the time the herd was 

diagnosed to the time the herd was depopulated and showed 24.1 percent of these mortalities were CWD positive. 3 For herds APHIS depopulated within 6 months of a CWD diagnosis, the average within herd CWD prevalence was 16.5

percent. 4 Sensitivity is over 99 percent. 5 Sensitivities range from 42 percent for 96GS deer to 76 percent for 96GG deer (Thomsen, et. al, 2012 and Keane et. al. 2009).
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 8003.1 

___________________________________________________________________ 

2 

the calculation6. IHC of RAMALT biopsy performs poorly in early infection, resulting in missing 

early cases.

After accounting for these variables, APHIS determined that IHC of RAMALT biopsy on five 

white-tailed deer representative of the mortality is appropriate to replace a missed mortality 

or a poor-quality submission in a herd. This value is based on a herd composition of 70 

percent genotype GG and 30 percent genotype GS at codon 96 and assumes the CWDpositive white-tailed deer in the herd are evenly divided between early- and late-stage CWD 

progression. This guidance document represents the Agency’s position on this topic and is 

intended solely as guidance. It does not have the force and effect of law, does not create, or 

confer any rights for or on any person, and does not bind the U.S. Department of Agriculture 

(USDA) or the public. Language suggesting that this guidance is mandatory (e.g., “shall,” 

“must,” “required,” or “requirement”) should not be construed as binding unless the terms 

quote from a statutory or regulatory requirement. The information this document contains 

may be made available to the public. While this document provides guidance for users 

outside APHIS, APHIS employees may not deviate from the directions provided herein 

without appropriate justification and supervisory concurrence.

Pursuant to the Congressional Review Act (5 U.S.C. § 801 et seq.), the Office of Information 

and Regulatory Affairs designated this rule as a non-major rule, as defined by 5 U.S.C. § 

804(2).

2. Document Status 

A. Review date: 6/30/2025. 

B. This is a new document.

3. Authority and References 

A. Authorities (Code of Federal Regulations (CFR)):

1) 7 CFR 371.4

2) 9 CFR 55.23

3) 9 CFR 55.8

B. References:

1) Chronic Wasting Disease Program Standards

C. Definitions:

6 Out of 588 accessions representing over 3,700 samples tested for CWD, 41 percent were early CWD cases (prion only 

detected in medial retropharyngeal lymph node) and 59 percent were late CWD cases (prion detected in the medial 

retropharyngeal lymph node and obex).
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 8003.1 

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3 

1) Approved State CWD HCP: A program operated by a State government for 

certification of cervid herds with respect to CWD that the Administrator has 

determined meets the requirements of 9 CFR 55.23(a).

2) CWD HCP: The Chronic Wasting Disease Herd Certification Program established by 9 

CFR part 55.The CWD HCP includes both herds directly enrolled in the CWD HCP and 

herds included based on their participation in Approved State CWD HCPs. 

3) Enrolled Herd: A herd that has enrolled in the CWD HCP and meets the minimum 

requirements defined in 9 CFR part 55. 

4) CWD-positive animal: An animal that has had a diagnosis of CWD established through 

official confirmatory testing conducted by the National Veterinary Services 

Laboratories (NVSL). 

5) CWD positive herd: A herd in which a CWD-positive animal resided at the time it was 

diagnosed and which has not been released from quarantine

6) SAHO: State animal health official or their designee.

7) AVIC: Area Veterinary in Charge or their designee. 

4. Audience 

VS employees, other federal and state agencies, and members of the public.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 8003.1 

___________________________________________________________________ 

4 

5. Guidance 

A. General

This document describes the process for approving herd owners to test live 

white-tailed deer for CWD by IHC using RAMALT biopsy, in lieu of a missed 

mortality test and the number and type of deer that must be tested. This policy 

only applies to white-tailed deer because of the lower sensitivity of the test and 

prolonged incubation period in elk7. The SAHO must be agreeable to this option 

before it is offered to the owner. The AVIC or the SAHO must review this guidance 

with the owner. 

B. Recordkeeping and Sampler Training

1) For each missing mortality or poor-quality sample submitted, the owner must 

document the reason it occurred, and the steps taken to prevent a 

recurrence. 

2) Samples collectors with repeated poor-quality or unusable sample 

submissions must take training as specified by the SAHO. Following this

training, if sampling errors continues, the SAHO should recommend the owner 

change sample collectors and advise them that ultimately, they are 

responsible for the quality of the samples submitted. 

C. Approval to use antemortem testing

1) The AVIC and SAHO must review the previous 3 years of inspection reports 

and testing history and conclude the owner is compliant with CWD HCP 

requirements as outlined in 9 CFR part 55 and the CWD Program Standards

before allowing the owner to follow the procedures outlined in this 

document. Specifically, owners with a history of repeatedly missing multiple 

mortalities and/or submitting poor-quality samples should not be considered 

for this deviation. The missing mortality and sample submission error should 

be 5 percent or less over 3 years (total number of missing mortalities + total 

number of poor-quality sample submissions) ÷ total number of mortalities × 

100). For herds of 100 or fewer animals, the entire herd history of missed 

mortalities and sample submissions can be used to calculate this error. The 

overall compliance history of the herd should also be considered.

2) The AVIC and the SAHO must agree in writing that the herd meets the criteria 

to replace a missed mortality or poor-quality sample with live white-tailed 

7 Moore et al. 2018.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 8003.1 

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5 

deer testing. Documentation of the decision, including rational, must be 

maintained in the herd file.

D. Sampling

1) White-tailed deer should be tested, as described below, for each white-tailed 

deer with a missed mortality or poor-quality sample submission. 

a. If the genotype of the white-tailed deer to be biopsied is not known: 

1. Sample five white-tailed deer that are between 2 to 4 years of age8 and

have the longest exposure to the white-tailed deer with the missed 

mortality or poor-quality sample submission. If there are not enough 

animals in this age group, sample animals nearest to that age range that 

are at least 2 years of age. 

b. If the genotype of the white-tailed deer to be biopsied is known:

1. The owner must provide genetic documentation and sample a total of five 

white-tailed deer with at least four white tailed deer with GG at codon 96. 

2. If the group of white-tailed deer does not contain four white-tailed deer 

with GG at codon 96, then the owner must test two white-tailed deer with 

GS at codon 96 to replace each codon 96GG white-tailed deer not tested. 

3. White-tailed deer that are antemortem sampled must be between 2 to 4 

years of age and have the longest exposure to the white-tailed deer with 

the missed mortality or poor-quality sample submission. If there are not 

enough animals in this age group, sample animals nearest to that age 

range that are at least 2 years of age.

E. All submitted rectal biopsy samples must have a minimum of six lymphoid follicles to 

be considered a valid diagnostic sample, and if not, the animal must be resampled or 

a similar animal substituted.

F. Sample collection must be done by a state or federal veterinarian or a licensed, 

accredited veterinarian under the supervision of a state or federal veterinarian, as 

described in the CWD Program Standards Section 5.3, and be submitted within 7 days 

of collection.

G. Liability and Associated Costs

1) The owner must pay all costs associated with sample collection, genetics, and 

diagnostic testing. 

8 The median age for white-tailed deer to be CWD-positive was 3 and average age 3.4 from over 1,600 samples taken from 2019 

to the present. The range was 0.5 to 15 years of age.
U.S. DEPARTMENT OF AGRICULTURE 

Marketing and Regulatory Programs

Animal and Plant Health Inspection Service

Veterinary Services 

VS Guidance 8003.1 

___________________________________________________________________ 

6 

2) The owner, and not the state, or APHIS, will bear the loss of any animal, function, 

or part of an animal that could arise because of handling or sample collection 

associated with the procedures specified in this document. 

3) Any method of chemical restraint used for testing shall be performed or 

administered by an individual who can legally purchase and administer chemical 

restraints in the state at the owner’s expense. 

H. Testing and Results

1) Unless the State’s NAHLN laboratory has a deviation approved by NVSL to test 

rectal biopsies the rectal biopsies must be sent to NVSL for CWD testing. 

2) If a positive result is found on a RAMALT biopsy, the herd will be put under 

quarantine by the State and will be designated a CWD positive herd.

6. Inquiries 

Please contact the APHIS Veterinary Services Ruminant Health Center, Cervid Health 

Program, at VS.SP.Cervid.Health@usda.gov with any questions about this guidance.